henrikstranneheim
commented
11 months ago hermes export tags --pipeline mip-dna 👍
θ65° [henrik.stranneheim@hasta:~] [S_base] 4s 2 $ hermes export tags --pipeline mip-dna
2023-12-21 09:26:22 hasta.scilifelab.se cg_hermes.cli.export[230205] INFO Running export tags for pipeline mip-dna
| Mip-dna tags | Mandatory | HK tags | Used by |
|-------------------------------------|-------------|----------------------------------|--------------|
| chanjo_sexcheck | False | chanjo, sex-check | scout |
| chromograph_upd, sites | False | chromograph, upd, sites | scout |
| chromograph_upd, regions | False | chromograph, upd, regions | scout |
| chromograph_cov, tcov | False | chromograph, tcov | scout |
| autozyg, chromograph_rhoviz | False | chromograph, autozyg | scout |
| fracsnp, chromograph_rhoviz | False | chromograph, fracsnp | scout |
| clinical, endvariantannotationblock | True | vcf-snv-clinical | scout |
| research, endvariantannotationblock | True | vcf-snv-research | scout |
| sv_str, expansionhunter | False | vcf-str | scout |
| str_variants, expansionhunter | False | expansionhunter, vcf-str | scout |
| expansionhunter, str_alignment | False | expansionhunter, bam | scout |
| variant_catalog, expansionhunter | False | expansionhunter, variant-catalog | scout |
| glnexus_merge | False | deepvariant, snv, vcf | storage |
| markduplicates | False | cram | scout |
| gatk_combinevariantcallsets | True | snv-gbcf, snv-bcf | genotype |
| baf, gens_generatedata | False | gens, fracsnp, bed | scout |
| cov, gens_generatedata | False | gens, coverage, bed | scout |
| me_merge_vcfs | False | retroseq, vcf | audit |
| me_filter, clinical | False | mobile-elements, clinical, vcf | scout |
| research, me_filter | False | mobile-elements, research, vcf | scout |
| mip_analyse, config | True | mip-analyse, config | cg, audit |
| mip_analyse, config_analysis | True | mip-config | cg, audit |
| mip_analyse, log | True | mip-log | audit |
| mip_analyse, pedigree | True | pedigree-yaml | audit |
| mip_analyse, pedigree_fam | True | pedigree | scout |
| mip_analyse, references_info | True | mip-analyse, reference-info | audit |
| sample_info, mip_analyse | True | sample-info | cg, audit |
| multiqc_ar, html | True | multiqc-html | scout |
| multiqc_ar, json | True | multiqc-json | vogue |
| mitodel | False | mitodel | scout |
| ped_check, peddy_ar | True | peddy, ped-check | audit, scout |
| peddy, peddy_ar | True | peddy, ped | audit, scout |
| sex_check, peddy_ar | True | peddy, sex-check | audit, scout |
| qccollect_ar, deliverable | True | qc-metrics, deliverable | audit |
| qccollect_ar, audit | True | qc-metrics, audit | audit |
| rhocall_viz | False | rhocall-viz | scout |
| coverage, sambamba_depth | True | coverage, sambamba-depth | chanjo |
| samtools_subsample_mt | False | bam-mt | scout |
| smncopynumbercaller | False | smn-calling | scout |
| star_caller | False | cyrius | scout |
| sv_combinevariantcallsets | True | sv-bcf | audit |
| sv_reformat, clinical | False | vcf-sv-clinical | scout |
| sv_reformat, research | False | vcf-sv-research | scout |
| telomerecat_ar | False | telomere-calling | scout |
| tiddit_coverage | False | tiddit-coverage, bigwig | scout |
| upd_ar, regions | False | upd, regions | scout |
| upd_ar, sites | False | upd, sites | scout |
| version_collect_ar | True | exe-ver | audit |
| vcf2cytosure_ar | False | vcf2cytosure | scout |
Description
Refactor to pep 0585.
Changed
How to prepare for test
uspaxabash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_hermes -t hermes -b refactor-to-PEP-0585How to test
Expected test outcome
Review
This version is a
Implementation Plan